Accelerated gradient based diffuse optical tomographic image reconstruction

Purpose: Fast reconstruction of interior optical parameter distribution using a new approach called Broyden-based model iterative image reconstruction (BMOBIIR) and adjoint Broyden-based MOBIIR (ABMOBIIR) of a tissue and a tissue mimicking phantom from boundary measurement data in diffuse optical tomography (DOT). Methods: DOT is a nonlinear and ill-posed inverse problem. Newton-based MOBIIR algorithm, which is generally used, requires repeated evaluation of the Jacobian which consumes bulk of the computation time for reconstruction. In this study, we propose a Broyden approach-based accelerated scheme for Jacobian computation and it is combined with conjugate gradient scheme (CGS) for fast reconstruction. The method makes explicit use of secant and adjoint information that can be obtained from forward solution of the diffusion equation. This approach reduces the computational time many fold by approximating the system Jacobian successively through low-rank updates. Results: Simulation studies have been carried out with single as well as multiple inhomogeneities. Algorithms are validated using an experimental study carried out on a pork tissue with fat acting as an inhomogeneity. The results obtained through the proposed BMOBIIR and ABMOBIIR approaches are compared with those of Newton-based MOBIIR algorithm. The mean squared error and execution time are used as metrics for comparing the results of reconstruction. Conclusions: We have shown through experimental and simulation studies that Broyden-based MOBIIR and adjoint Broyden-based methods are capable of reconstructing single as well as multiple inhomogeneities in tissue and a tissue-mimicking phantom. Broyden MOBIIR and adjoint Broyden MOBIIR methods are computationally simple and they result in much faster implementations because they avoid direct evaluation of Jacobian. The image reconstructions have been carried out with different initial values using Newton, Broyden, and adjoint Broyden approaches. These algorithms work well when the initial guess is close to the true solution. However, when initial guess is far away from true solution, Newton-based MOBIIR gives better reconstructed images. The proposed methods are found to be stable with noisy measurement data. (C) 2011 American Association of Physicists in Medicine. DOI: 10.1118/1.3531572]

Fuzzy Logic-Based Approaches in Water Resource System Modelling

Recent research in modelling uncertainty in water resource systems has highlighted the use of fuzzy logic-based approaches. A number of research contributions exist in the literature that deal with uncertainty in water resource systems including fuzziness, subjectivity, imprecision and lack of adequate data. This chapter presents a broad overview of the fuzzy logic-based approaches adopted in addressing uncertainty in water resource systems modelling. Applications of fuzzy rule-based systems and fuzzy optimisation are then discussed. Perspectives on the scope for further research are presented.

A Gradient-Based Comparison Measure for Visual analysis of Multifield Data

We introduce a multifield comparison measure for scalar fields that helps in studying relations between them. The comparison measure is insensitive to noise in the scalar fields and to noise in their gradients. Further, it can be computed robustly and efficiently. Results from the visual analysis of various data sets from climate science and combustion applications demonstrate the effective use of the measure.

Process Development for Functionalization of Cotton with Silver Nanoparticles Synthesized by Bio-based Approaches

Cotton is a widely used raw material for textiles but drawbacks regarding their poor mechanical properties often limit their applications as functional materials. The present investigation involved process development for one step coating of cotton with silver nanoparticles (SNP) synthesized using Azadirachta indica and Citrus limon extract to develop functional textiles. Addition of starch to functional textiles led to efficient binding of nanoparticles to fabric and led to drastic decrease in release of silver from fabricated textiles after ten washing cycles enhancing their environment friendliness. Differential scanning calorimetry, scanning electron microscopy, FT-IR analysis and mechanical studies demonstrated efficient binding of nanoparticles to fabric through bio-based processes. The functionalized textiles developed by the bio-based methods showed significant antibacterial activity against E. coli and S. aureus (with 99% microbial reduction). Present work offers a simple procedure for coating SNP using bio-based approaches with promising applications in specialized functions.

Swarm intelligence-based solver for parameter estimation of laboratory through-diffusion transport of contaminants

Theoretical approaches are of fundamental importance to predict the potential impact of waste disposal facilities on ground water contamination. Appropriate design parameters are generally estimated be fitting theoretical models to data gathered from field monitoring or laboratory experiments. Transient through-diffusion tests are generally conducted in the laboratory to estimate the mass transport parameters of the proposed barrier material. Thes parameters are usually estimated either by approximate eye-fitting calibration or by combining the solution of the direct problem with any available gradient-based techniques. In this work, an automated, gradient-free solver is developed to estimate the mass transport parameters of a transient through-diffusion model. The proposed inverse model uses a particle swarm optimization (PSO) algorithm that is based on the social behavior of animals searching for food sources. The finite difference numerical solution of the forward model is integrated with the PSO algorithm to solve the inverse problem of parameter estimation. The working principle of the new solver is demonstrated and mass transport parameters are estimated from laboratory through-diffusion experimental data. An inverse model based on the standard gradient-based technique is formulated to compare with the proposed solver. A detailed comparative study is carried out between conventional methods and the proposed solver. The present automated technique is found to be very efficient and robust. The mass transport parameters are obtained with great precision.

Strength design of composite beam using gradient and particle swarm optimization

This work addresses the optimum design of a composite box-beam structure subject to strength constraints. Such box-beams are used as the main load carrying members of helicopter rotor blades. A computationally efficient analytical model for box-beam is used. Optimal ply orientation angles are sought which maximize the failure margins with respect to the applied loading. The Tsai-Wu-Hahn failure criterion is used to calculate the reserve factor for each wall and ply and the minimum reserve factor is maximized. Ply angles are used as design variables and various cases of initial starting design and loadings are investigated. Both gradient-based and particle swarm optimization (PSO) methods are used. It is found that the optimization approach leads to the design of a box-beam with greatly improved reserve factors which can be useful for helicopter rotor structures. While the PSO yields globally best designs, the gradient-based method can also be used with appropriate starting designs to obtain useful designs efficiently. (C) 2006 Elsevier Ltd. All rights reserved.

A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization

We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa–Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.

A Deterministic Optimization Approach to Protein Sequence Design Using Continuous Models

Determining the sequence of amino acid residues in a heteropolymer chain of a protein with a given conformation is a discrete combinatorial problem that is not generally amenable for gradient-based continuous optimization algorithms. In this paper we present a new approach to this problem using continuous models. In this modeling, continuous "state functions" are proposed to designate the type of each residue in the chain. Such a continuous model helps define a continuous sequence space in which a chosen criterion is optimized to find the most appropriate sequence. Searching a continuous sequence space using a deterministic optimization algorithm makes it possible to find the optimal sequences with much less computation than many other approaches. The computational efficiency of this method is further improved by combining it with a graph spectral method, which explicitly takes into account the topology of the desired conformation and also helps make the combined method more robust. The continuous modeling used here appears to have additional advantages in mimicking the folding pathways and in creating the energy landscapes that help find sequences with high stability and kinetic accessibility. To illustrate the new approach, a widely used simplifying assumption is made by considering only two types of residues: hydrophobic (H) and polar (P). Self-avoiding compact lattice models are used to validate the method with known results in the literature and data that can be practically obtained by exhaustive enumeration on a desktop computer. We also present examples of sequence design for the HP models of some real proteins, which are solved in less than five minutes on a single-processor desktop computer Some open issues and future extensions are noted.

Unified Vdd Vth Optimization Based DVFM Controller for a Logic Block

In this paper analytical expressions for optimal Vdd and Vth to minimize energy for a given speed constraint are derived. These expressions are based on the EKV model for transistors and are valid in both strong inversion and sub threshold regions. The effect of gate leakage on the optimal Vdd and Vth is analyzed. A new gradient based algorithm for controlling Vdd and Vth based on delay and power monitoring results is proposed. A Vdd-Vth controller which uses the algorithm to dynamically control the supply and threshold voltage of a representative logic block (sum of absolute difference computation of an MPEG decoder) is designed. Simulation results using 65 nm predictive technology models are given.

Indicator-based urban sustainability-A review

Sustainability has emerged as one of the important planning concepts from its beginnings in economics and ecological thinking, and has widely been applied to assessing urban development. Different methods, techniques and instruments for urban sustainability assessment that help determine how cities can become more sustainable have emerged over a period of time. Among these, indicator-based approaches contribute to building of sustainable self-regulated systems that integrate development and environment protection. Hence, these provide a solid foundation for decision-making at all levels and are being increasingly used. The present paper builds on the background of the available literature and suggests the need for benchmarking indicator-based approach in a given urban area and incorporating various local issues, thus enhancing the long-term sustainability of cities which can be developed by introducing sustainability indicators into the urban planning process. (C) 2013 International Energy Initiative. Published by Elsevier Inc. All rights reserved.

Training-Based Antenna Selection for PER Minimization: A POMDP Approach

This paper considers the problem of receive antenna selection (AS) in a multiple-antenna communication system having a single radio-frequency (RF) chain. The AS decisions are based on noisy channel estimates obtained using known pilot symbols embedded in the data packets. The goal here is to minimize the average packet error rate (PER) by exploiting the known temporal correlation of the channel. As the underlying channels are only partially observed using the pilot symbols, the problem of AS for PER minimization is cast into a partially observable Markov decision process (POMDP) framework. Under mild assumptions, the optimality of a myopic policy is established for the two-state channel case. Moreover, two heuristic AS schemes are proposed based on a weighted combination of the estimated channel states on the different antennas. These schemes utilize the continuous valued received pilot symbols to make the AS decisions, and are shown to offer performance comparable to the POMDP approach, which requires one to quantize the channel and observations to a finite set of states. The performance improvement offered by the POMDP solution and the proposed heuristic solutions relative to existing AS training-based approaches is illustrated using Monte Carlo simulations.

Towards rational synthesis of inorganic solids

There have been major advances in the past couple of years in the rational synthesis of inorganic solids: synthesis of mercury-based superconducting cuprates showing transition temperatures up to 150 K; ZrP2-xVxO7 solid solutions showing zero or negative thermal expansion; copper oxides possessing ladder structures such as La1-xSrxCuO2.5; synthesis of mesoporous oxide materials having adjustable pore size in the range 15-100 Angstrom; and synthesis of a molecular ferromagnet showing a critical temperature of 18.6 K. Despite great advances in probing the structures of solids and measurement of their physical properties, the design and synthesis of inorganic solids possessing desired structures and properties remain a challenge today. With the availability of a variety of mild chemistry-based approaches, kinetic control of synthetic pathways is becoming increasingly possible, which, it is hoped, will eventually make rational design of inorganic solids a reality.

Computational systems approach for drug target discovery

Importance of the field: The shift in focus from ligand based design approaches to target based discovery over the last two to three decades has been a major milestone in drug discovery research. Currently, it is witnessing another major paradigm shift by leaning towards the holistic systems based approaches rather the reductionist single molecule based methods. The effect of this new trend is likely to be felt strongly in terms of new strategies for therapeutic intervention, new targets individually and in combinations, and design of specific and safer drugs. Computational modeling and simulation form important constituents of new-age biology because they are essential to comprehend the large-scale data generated by high-throughput experiments and to generate hypotheses, which are typically iterated with experimental validation. Areas covered in this review: This review focuses on the repertoire of systems-level computational approaches currently available for target identification. The review starts with a discussion on levels of abstraction of biological systems and describes different modeling methodologies that are available for this purpose. The review then focuses on how such modeling and simulations can be applied for drug target discovery. Finally, it discusses methods for studying other important issues such as understanding targetability, identifying target combinations and predicting drug resistance, and considering them during the target identification stage itself. What the reader will gain: The reader will get an account of the various approaches for target discovery and the need for systems approaches, followed by an overview of the different modeling and simulation approaches that have been developed. An idea of the promise and limitations of the various approaches and perspectives for future development will also be obtained. Take home message: Systems thinking has now come of age enabling a `bird's eye view' of the biological systems under study, at the same time allowing us to `zoom in', where necessary, for a detailed description of individual components. A number of different methods available for computational modeling and simulation of biological systems can be used effectively for drug target discovery.

Simultaneous material selection and geometry design of statically determinate trusses using continuous optimization

In this work, we explore simultaneous geometry design and material selection for statically determinate trusses by posing it as a continuous optimization problem. The underlying principles of our approach are structural optimization and Ashby’s procedure for material selection from a database. For simplicity and ease of initial implementation, only static loads are considered in this work with the intent of maximum stiffness, minimum weight/cost, and safety against failure. Safety of tensile and compression members in the truss is treated differently to prevent yield and buckling failures, respectively. Geometry variables such as lengths and orientations of members are taken to be the design variables in an assumed layout. Areas of cross-section of the members are determined to satisfy the failure constraints in each member. Along the lines of Ashby’s material indices, a new design index is derived for trusses. The design index helps in choosing the most suitable material for any geometry of the truss. Using the design index, both the design space and the material database are searched simultaneously using gradient-based optimization algorithms. The important feature of our approach is that the formulated optimization problem is continuous, although the material selection from a database is an inherently discrete problem. A few illustrative examples are included. It is observed that the method is capable of determining the optimal topology in addition to optimal geometry when the assumed layout contains more links than are necessary for optimality.